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<h1 class="epydoc">Source Code for <a href="ijtools-module.html">Module ijtools</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># Copyright (c) 2009, Ricardo Henriques</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"># All rights reserved.</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"># Redistribution and use in source and binary forms, with or without</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-comment"># modification, are permitted provided that the following conditions are met:</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment">#    * Redistributions of source code must retain the above copyright notice,</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-comment">#      this list of conditions and the following disclaimer.</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment">#    * Redistributions in binary form must reproduce the above copyright</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-comment">#      notice, this list of conditions and the following disclaimer in the</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-comment">#      documentation and/or other materials provided with the distribution.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-comment">#    * Neither the name of the author nor the names of its contributors</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-comment">#      may be used to endorse or promote products derived from this software</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-comment">#      without specific prior written permission.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-comment"># THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-comment"># AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-comment"># IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-comment"># ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-comment"># LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-comment"># CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-comment"># SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-comment"># INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-comment"># CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-comment"># ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-comment"># THE POSSIBILITY OF SUCH DAMAGE.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-docstring">"Interface to ImageJ API, making functions more 'Pythonic'"</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"> </tt>
<a name="getImage"></a><div id="getImage-def"><a name="L28"></a><tt class="py-lineno"> 28</tt> <a class="py-toggle" href="#" id="getImage-toggle" onclick="return toggle('getImage');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#getImage">getImage</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getImage-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="getImage-expanded"><a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring">    Returns a reference to the active image.</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: ImagePlus</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Function ijtools.getImage()=ijtools-module.html#getImage"><a title="ijtools.getImage" class="py-name" href="#" onclick="return doclink('link-0', 'getImage', 'link-0');">getImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"> </tt>
<a name="getPixels"></a><div id="getPixels-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="getPixels-toggle" onclick="return toggle('getPixels');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#getPixels">getPixels</a><tt class="py-op">(</tt><tt class="py-param">slice</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">im</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getPixels-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="getPixels-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-docstring">    Returns the pixels of the given ImageJ as a python 2D list.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt class="py-docstring">    @param slice: get pixels from the specified slice number, if 'None' use current</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-docstring">    selected slice.</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-docstring">    @type slice: int or None</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-docstring">    @param im: ImageJ ImagePlus to use, if 'None' use the current select image.</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring">    @type im: ImageJ ImagePlus</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring">    @return: python 2D list of ints</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: list of lists of ints</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Function ijtools.error()=ijtools-module.html#error"><a title="ijtools.error" class="py-name" href="#" onclick="return doclink('link-1', 'error', 'link-1');">error</a></tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">im</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">im</tt><tt class="py-op">=</tt><tt id="link-2" class="py-name"><a title="ijtools.getImage" class="py-name" href="#" onclick="return doclink('link-2', 'getImage', 'link-0');">getImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">slice</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">slice</tt><tt class="py-op">=</tt><tt class="py-name">im</tt><tt class="py-op">.</tt><tt class="py-name">getCurrentSlice</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">    <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-name">im</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Function ijtools.getBitDepth()=ijtools-module.html#getBitDepth"><a title="ijtools.getBitDepth" class="py-name" href="#" onclick="return doclink('link-3', 'getBitDepth', 'link-3');">getBitDepth</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">    <tt class="py-name">proc</tt><tt class="py-op">=</tt><tt class="py-name">im</tt><tt class="py-op">.</tt><tt class="py-name">getImageStack</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">getProcessor</tt><tt class="py-op">(</tt><tt class="py-name">slice</tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">    <tt class="py-comment">#im.lock()</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">type</tt><tt class="py-op">==</tt><tt class="py-number">24</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">        <tt class="py-comment">#im.unlock()</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt id="link-4" class="py-name"><a title="ijtools.error" class="py-name" href="#" onclick="return doclink('link-4', 'error', 'link-1');">error</a></tt><tt class="py-op">.</tt><tt class="py-name">ImageTypeNotSupported</tt><tt class="py-op">,</tt> <tt class="py-string">"RGB images not supported"</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">type</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-number">8</tt><tt class="py-op">,</tt> <tt class="py-number">16</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-name">pixels</tt><tt class="py-op">=</tt><tt class="py-name">proc</tt><tt class="py-op">.</tt><tt class="py-name">getIntArray</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-name">pixels</tt><tt class="py-op">=</tt><tt class="py-name">proc</tt><tt class="py-op">.</tt><tt class="py-name">getFloatArray</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">    <tt class="py-comment">#im.unlock()</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">    <tt class="py-name">pixels</tt><tt class="py-op">=</tt><tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">pixels</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pixels</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-name">pixels</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">list</tt><tt class="py-op">(</tt><tt class="py-name">pixels</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">pixels</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"> </tt>
<a name="setPixels"></a><div id="setPixels-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="setPixels-toggle" onclick="return toggle('setPixels');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#setPixels">setPixels</a><tt class="py-op">(</tt><tt class="py-param">pixels</tt><tt class="py-op">,</tt> <tt class="py-param">slice</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">im</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="setPixels-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="setPixels-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring">    Sets the given 2D pixel list into the image.</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-docstring">    @param pixels: python 2D list of ints</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-docstring">    @type pixels: list of lists of ints</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt class="py-docstring">    @param slice: set pixels on the specified slice number, if 'None' use current</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-docstring">    @type slice: int or None</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-docstring">    @param im: ImageJ ImagePlus to use, if 'None' use the current select image.</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-docstring">    @type im: ImageJ ImagePlus</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="ijtools.error" class="py-name" href="#" onclick="return doclink('link-5', 'error', 'link-1');">error</a></tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">im</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">im</tt><tt class="py-op">=</tt><tt id="link-6" class="py-name"><a title="ijtools.getImage" class="py-name" href="#" onclick="return doclink('link-6', 'getImage', 'link-0');">getImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">slice</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">slice</tt><tt class="py-op">=</tt><tt class="py-name">im</tt><tt class="py-op">.</tt><tt class="py-name">getCurrentSlice</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">    <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-name">im</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="ijtools.getBitDepth" class="py-name" href="#" onclick="return doclink('link-7', 'getBitDepth', 'link-3');">getBitDepth</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">    <tt class="py-name">proc</tt><tt class="py-op">=</tt><tt class="py-name">im</tt><tt class="py-op">.</tt><tt class="py-name">getImageStack</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">getProcessor</tt><tt class="py-op">(</tt><tt class="py-name">slice</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">    <tt class="py-comment">#im.lock()</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">type</tt><tt class="py-op">==</tt><tt class="py-number">24</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">        <tt class="py-comment">#im.unlock()</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt id="link-8" class="py-name"><a title="ijtools.error" class="py-name" href="#" onclick="return doclink('link-8', 'error', 'link-1');">error</a></tt><tt class="py-op">.</tt><tt class="py-name">ImageTypeNotSupported</tt><tt class="py-op">,</tt> <tt class="py-string">"RGB images not supported"</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">type</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-number">8</tt><tt class="py-op">,</tt> <tt class="py-number">16</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-name">proc</tt><tt class="py-op">.</tt><tt class="py-name">setIntArray</tt><tt class="py-op">(</tt><tt class="py-name">pixels</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-name">proc</tt><tt class="py-op">.</tt><tt class="py-name">setFloatArray</tt><tt class="py-op">(</tt><tt class="py-name">pixels</tt><tt class="py-op">)</tt> </tt>
</div><a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">    <tt class="py-comment">#im.unlock()</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"> </tt>
<a name="getBitDepth"></a><div id="getBitDepth-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="getBitDepth-toggle" onclick="return toggle('getBitDepth');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#getBitDepth">getBitDepth</a><tt class="py-op">(</tt><tt class="py-param">im</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">numpy</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getBitDepth-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="getBitDepth-expanded"><a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-docstring">    Returns the bit depth of the given image.</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-docstring">    @param im: ImageJ ImagePlus to use, if 'None' use the current select image.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-docstring">    @type im: ImageJ ImagePlus</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"><tt class="py-docstring">    @param numpy: if true, return bit depth on Numpy dtype compatible format.</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt class="py-docstring">    @type numpy: bool</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: int or str</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name"><a title="ijtools.error" class="py-name" href="#" onclick="return doclink('link-9', 'error', 'link-1');">error</a></tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">im</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">im</tt><tt class="py-op">=</tt><tt id="link-10" class="py-name"><a title="ijtools.getImage" class="py-name" href="#" onclick="return doclink('link-10', 'getImage', 'link-0');">getImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">    <tt class="py-name">bd</tt><tt class="py-op">=</tt><tt class="py-name">im</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="ijtools.getBitDepth" class="py-name" href="#" onclick="return doclink('link-11', 'getBitDepth', 'link-3');">getBitDepth</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt>  </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">numpy</tt><tt class="py-op">==</tt><tt class="py-name">False</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">bd</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">bd</tt><tt class="py-op">==</tt><tt class="py-number">8</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-string">'uint8'</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">bd</tt><tt class="py-op">==</tt><tt class="py-number">16</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-string">'uint16'</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">bd</tt><tt class="py-op">==</tt><tt class="py-number">32</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-string">'float'</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt id="link-12" class="py-name"><a title="ijtools.error" class="py-name" href="#" onclick="return doclink('link-12', 'error', 'link-1');">error</a></tt><tt class="py-op">.</tt><tt class="py-name">ImageTypeNotSupported</tt><tt class="py-op">,</tt> <tt class="py-string">"RGB images not supported"</tt> </tt>
</div><a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">     </tt>
<a name="nSlices"></a><div id="nSlices-def"><a name="L110"></a><tt class="py-lineno">110</tt> <a class="py-toggle" href="#" id="nSlices-toggle" onclick="return toggle('nSlices');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#nSlices">nSlices</a><tt class="py-op">(</tt><tt class="py-param">im</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>  </tt>
</div><a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line"><tt class="py-docstring">    Returns the number of slices on the image.</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line"><tt class="py-docstring">    @param im: ImageJ ImagePlus to use, if 'None' use the current select image.</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line"><tt class="py-docstring">    @type im: ImageJ ImagePlus</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: int</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">im</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">im</tt><tt class="py-op">=</tt><tt id="link-13" class="py-name"><a title="ijtools.getImage" class="py-name" href="#" onclick="return doclink('link-13', 'getImage', 'link-0');">getImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">im</tt><tt class="py-op">.</tt><tt class="py-name">getNSlices</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">     </tt>
<a name="setSlice"></a><div id="setSlice-def"><a name="L121"></a><tt class="py-lineno">121</tt> <a class="py-toggle" href="#" id="setSlice-toggle" onclick="return toggle('setSlice');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#setSlice">setSlice</a><tt class="py-op">(</tt><tt class="py-param">n</tt><tt class="py-op">,</tt> <tt class="py-param">im</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="setSlice-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="setSlice-expanded"><a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line"><tt class="py-docstring">    Sets the selected slice to 'n'.</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"><tt class="py-docstring">    @type n: int</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"><tt class="py-docstring">    @param im: ImageJ ImagePlus to use, if 'None' use the current select image.</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line"><tt class="py-docstring">    @type im: ImageJ ImagePlus</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">im</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">im</tt><tt class="py-op">=</tt><tt id="link-14" class="py-name"><a title="ijtools.getImage" class="py-name" href="#" onclick="return doclink('link-14', 'getImage', 'link-0');">getImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">    <tt class="py-name">im</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Function ijtools.setSlice()=ijtools-module.html#setSlice"><a title="ijtools.setSlice" class="py-name" href="#" onclick="return doclink('link-15', 'setSlice', 'link-15');">setSlice</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
</div><a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">     </tt>
<a name="getShape"></a><div id="getShape-def"><a name="L133"></a><tt class="py-lineno">133</tt> <a class="py-toggle" href="#" id="getShape-toggle" onclick="return toggle('getShape');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#getShape">getShape</a><tt class="py-op">(</tt><tt class="py-param">im</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getShape-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="getShape-expanded"><a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"><tt class="py-docstring">    Return the image shape as a tuple of (nslices, width, height).</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"><tt class="py-docstring">    @param im: ImageJ ImagePlus to use, if 'None' use the current select image.</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"><tt class="py-docstring">    @type im: ImageJ ImagePlus</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: (int, int, int)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">im</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">im</tt><tt class="py-op">=</tt><tt id="link-16" class="py-name"><a title="ijtools.getImage" class="py-name" href="#" onclick="return doclink('link-16', 'getImage', 'link-0');">getImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">im</tt><tt class="py-op">.</tt><tt class="py-name">getNSlices</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">im</tt><tt class="py-op">.</tt><tt class="py-name">getWidth</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">im</tt><tt class="py-op">.</tt><tt class="py-name">getHeight</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">     </tt>
<a name="showMessage"></a><div id="showMessage-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="showMessage-toggle" onclick="return toggle('showMessage');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#showMessage">showMessage</a><tt class="py-op">(</tt><tt class="py-param">msg</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="showMessage-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="showMessage-expanded"><a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line"><tt class="py-docstring">    Displays a message in a dialog box titled "Message".</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line"><tt class="py-docstring">    @param msg: text to be shown</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line"><tt class="py-docstring">    @type msg: str</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line"><tt class="py-docstring">    @param title: dialog box title</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line"><tt class="py-docstring">    @type title: str</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">title</tt><tt class="py-op">!=</tt><tt class="py-string">""</tt><tt class="py-op">:</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Function ijtools.showMessage()=ijtools-module.html#showMessage"><a title="ijtools.showMessage" class="py-name" href="#" onclick="return doclink('link-17', 'showMessage', 'link-17');">showMessage</a></tt><tt class="py-op">(</tt><tt class="py-name">title</tt><tt class="py-op">,</tt> <tt class="py-name">msg</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="ijtools.showMessage" class="py-name" href="#" onclick="return doclink('link-18', 'showMessage', 'link-17');">showMessage</a></tt><tt class="py-op">(</tt><tt class="py-name">msg</tt><tt class="py-op">)</tt> </tt>
</div><a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line"> </tt>
<a name="showStatus"></a><div id="showStatus-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="showStatus-toggle" onclick="return toggle('showStatus');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#showStatus">showStatus</a><tt class="py-op">(</tt><tt class="py-param">msg</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="showStatus-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="showStatus-expanded"><a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line"><tt class="py-docstring">    Displays a message in the ImageJ status bar.</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line"><tt class="py-docstring">    @param msg: text to be shown</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line"><tt class="py-docstring">    @type msg: str</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">    <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Function ijtools.showStatus()=ijtools-module.html#showStatus"><a title="ijtools.showStatus" class="py-name" href="#" onclick="return doclink('link-19', 'showStatus', 'link-19');">showStatus</a></tt><tt class="py-op">(</tt><tt class="py-name">msg</tt><tt class="py-op">)</tt> </tt>
</div><a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line"> </tt>
<a name="showProgress"></a><div id="showProgress-def"><a name="L169"></a><tt class="py-lineno">169</tt> <a class="py-toggle" href="#" id="showProgress-toggle" onclick="return toggle('showProgress');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#showProgress">showProgress</a><tt class="py-op">(</tt><tt class="py-param">index</tt><tt class="py-op">,</tt> <tt class="py-param">finalIndex</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="showProgress-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="showProgress-expanded"><a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line"><tt class="py-docstring">    Shows the progress bar in the ImageJ window:</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"><tt class="py-docstring">    If finalIndex==None -&gt; Updates the progress bar, where 0&lt;=progress&lt;=1.0.</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"><tt class="py-docstring">    If finalIndex!=None -&gt; Updates the progress bar, where the length of the bar</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line"><tt class="py-docstring">    is set to (currentValue+1)/finalValue of the maximum bar length.</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line"><tt class="py-docstring">    @type index: number</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line"><tt class="py-docstring">    @type finalIndex: int</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">finalIndex</tt><tt class="py-op">!=</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">        <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Function ijtools.showProgress()=ijtools-module.html#showProgress"><a title="ijtools.showProgress" class="py-name" href="#" onclick="return doclink('link-20', 'showProgress', 'link-20');">showProgress</a></tt><tt class="py-op">(</tt><tt class="py-name">index</tt><tt class="py-op">,</tt> <tt class="py-name">finalIndex</tt><tt class="py-op">)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">        <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="ijtools.showProgress" class="py-name" href="#" onclick="return doclink('link-21', 'showProgress', 'link-20');">showProgress</a></tt><tt class="py-op">(</tt><tt class="py-name">index</tt><tt class="py-op">)</tt> </tt>
</div><a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">         </tt>
<a name="getString"></a><div id="getString-def"><a name="L187"></a><tt class="py-lineno">187</tt> <a class="py-toggle" href="#" id="getString-toggle" onclick="return toggle('getString');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#getString">getString</a><tt class="py-op">(</tt><tt class="py-param">prompt</tt><tt class="py-op">,</tt> <tt class="py-param">defaultString</tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getString-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="getString-expanded"><a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line"><tt class="py-docstring">    Allows the user to enter a string in a dialog box.</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line"><tt class="py-docstring">    @type prompt: str</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"><tt class="py-docstring">    @type defaultString: str</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Function ijtools.getString()=ijtools-module.html#getString"><a title="ijtools.getString" class="py-name" href="#" onclick="return doclink('link-22', 'getString', 'link-22');">getString</a></tt><tt class="py-op">(</tt><tt class="py-name">prompt</tt><tt class="py-op">,</tt> <tt class="py-name">defaultString</tt><tt class="py-op">)</tt> </tt>
</div><a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line"> </tt>
<a name="getNumber"></a><div id="getNumber-def"><a name="L198"></a><tt class="py-lineno">198</tt> <a class="py-toggle" href="#" id="getNumber-toggle" onclick="return toggle('getNumber');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#getNumber">getNumber</a><tt class="py-op">(</tt><tt class="py-param">prompt</tt><tt class="py-op">,</tt> <tt class="py-param">defaultValue</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getNumber-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="getNumber-expanded"><a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line"><tt class="py-docstring">    Allows the user to enter a string in a dialog box.</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line"><tt class="py-docstring">    @type prompt: str</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line"><tt class="py-docstring">    @type defaultValue: number </tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Function ijtools.getNumber()=ijtools-module.html#getNumber"><a title="ijtools.getNumber" class="py-name" href="#" onclick="return doclink('link-23', 'getNumber', 'link-23');">getNumber</a></tt><tt class="py-op">(</tt><tt class="py-name">prompt</tt><tt class="py-op">,</tt> <tt class="py-name">defaultValue</tt><tt class="py-op">)</tt> </tt>
</div><a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line"> </tt>
<a name="getPrefs"></a><div id="getPrefs-def"><a name="L209"></a><tt class="py-lineno">209</tt> <a class="py-toggle" href="#" id="getPrefs-toggle" onclick="return toggle('getPrefs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#getPrefs">getPrefs</a><tt class="py-op">(</tt><tt class="py-param">key</tt><tt class="py-op">,</tt> <tt class="py-param">default</tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getPrefs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="getPrefs-expanded"><a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line"><tt class="py-docstring">    Uses the keyword key to retrieve a string from the preferences file.</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line"><tt class="py-docstring">    @param key: keyword associated to the preference</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line"><tt class="py-docstring">    @type key: str</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line"><tt class="py-docstring">    @param default: default value of the preference</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line"><tt class="py-docstring">    @type default: str</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line"><tt class="py-docstring">    @return: preference</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: str</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">Prefs</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">Prefs</tt><tt class="py-op">.</tt><tt class="py-name">get</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">default</tt><tt class="py-op">)</tt> </tt>
</div><a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">     </tt>
<a name="setPrefs"></a><div id="setPrefs-def"><a name="L223"></a><tt class="py-lineno">223</tt> <a class="py-toggle" href="#" id="setPrefs-toggle" onclick="return toggle('setPrefs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#setPrefs">setPrefs</a><tt class="py-op">(</tt><tt class="py-param">key</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="setPrefs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="setPrefs-expanded"><a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line"><tt class="py-docstring">    Saves value in the preferences file using the keyword key.</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line"><tt class="py-docstring">    @param key: keyword associated to the preference</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"><tt class="py-docstring">    @type key: str</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line"><tt class="py-docstring">    @param value: value to store in the preferences</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line"><tt class="py-docstring">    @type value: str    </tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">Prefs</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">    <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">Prefs</tt><tt class="py-op">.</tt><tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">value</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">    <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">Prefs</tt><tt class="py-op">.</tt><tt class="py-name">savePreferences</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">     </tt>
<a name="getTitle"></a><div id="getTitle-def"><a name="L237"></a><tt class="py-lineno">237</tt> <a class="py-toggle" href="#" id="getTitle-toggle" onclick="return toggle('getTitle');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#getTitle">getTitle</a><tt class="py-op">(</tt><tt class="py-param">im</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getTitle-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="getTitle-expanded"><a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line"><tt class="py-docstring">    Returns the image name.</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line"><tt class="py-docstring">    @param im: ImageJ ImagePlus to use, if 'None' use the current select image.</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line"><tt class="py-docstring">    @type im: ImageJ ImagePlus    </tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line"><tt class="py-docstring">    @return: image name</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: str</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">im</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">im</tt><tt class="py-op">=</tt><tt id="link-24" class="py-name"><a title="ijtools.getImage" class="py-name" href="#" onclick="return doclink('link-24', 'getImage', 'link-0');">getImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">im</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Function ijtools.getTitle()=ijtools-module.html#getTitle"><a title="ijtools.getTitle" class="py-name" href="#" onclick="return doclink('link-25', 'getTitle', 'link-25');">getTitle</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">     </tt>
<a name="run"></a><div id="run-def"><a name="L249"></a><tt class="py-lineno">249</tt> <a class="py-toggle" href="#" id="run-toggle" onclick="return toggle('run');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#run">run</a><tt class="py-op">(</tt><tt class="py-param">command</tt><tt class="py-op">,</tt> <tt class="py-param">options</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">im</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="run-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="run-expanded"><a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line"><tt class="py-docstring">    Runs an ImageJ command using the specified image and options.</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line"><tt class="py-docstring">    @type command: str</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line"><tt class="py-docstring">    @type options: str</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line"><tt class="py-docstring">    @param im: ImageJ ImagePlus to use, if 'None' use the current select image.</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line"><tt class="py-docstring">    @type im: ImageJ ImagePlus</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">options</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Function ijtools.run()=ijtools-module.html#run"><a title="ijtools.run" class="py-name" href="#" onclick="return doclink('link-26', 'run', 'link-26');">run</a></tt><tt class="py-op">(</tt><tt class="py-name">command</tt><tt class="py-op">)</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">im</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="ijtools.run" class="py-name" href="#" onclick="return doclink('link-27', 'run', 'link-26');">run</a></tt><tt class="py-op">(</tt><tt class="py-name">command</tt><tt class="py-op">,</tt> <tt class="py-name">options</tt><tt class="py-op">)</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="ijtools.run" class="py-name" href="#" onclick="return doclink('link-28', 'run', 'link-26');">run</a></tt><tt class="py-op">(</tt><tt class="py-name">im</tt><tt class="py-op">,</tt> <tt class="py-name">command</tt><tt class="py-op">,</tt> <tt class="py-name">options</tt><tt class="py-op">)</tt> </tt>
</div><a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">     </tt>
<a name="close"></a><div id="close-def"><a name="L264"></a><tt class="py-lineno">264</tt> <a class="py-toggle" href="#" id="close-toggle" onclick="return toggle('close');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#close">close</a><tt class="py-op">(</tt><tt class="py-param">im</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="close-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="close-expanded"><a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line"><tt class="py-docstring">    Closes the image and sets the pixel arrays to null.</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line"><tt class="py-docstring">    @param im: ImageJ ImagePlus to use, if 'None' use the current select image.</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line"><tt class="py-docstring">    @type im: ImageJ ImagePlus</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">im</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">im</tt><tt class="py-op">=</tt><tt id="link-29" class="py-name"><a title="ijtools.getImage" class="py-name" href="#" onclick="return doclink('link-29', 'getImage', 'link-0');">getImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">    <tt class="py-name">im</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Function ijtools.close()=ijtools-module.html#close"><a title="ijtools.close" class="py-name" href="#" onclick="return doclink('link-30', 'close', 'link-30');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line">     </tt>
<a name="updateAndDraw"></a><div id="updateAndDraw-def"><a name="L275"></a><tt class="py-lineno">275</tt> <a class="py-toggle" href="#" id="updateAndDraw-toggle" onclick="return toggle('updateAndDraw');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#updateAndDraw">updateAndDraw</a><tt class="py-op">(</tt><tt class="py-param">im</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="updateAndDraw-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="updateAndDraw-expanded"><a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line"><tt class="py-docstring">    Updates the image from the pixel data in its associated ImageProcessor,</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line"><tt class="py-docstring">    then displays it.</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line"><tt class="py-docstring">    @param im: ImageJ ImagePlus to use, if 'None' use the current select image.</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line"><tt class="py-docstring">    @type im: ImageJ ImagePlus</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None    </tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">im</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">im</tt><tt class="py-op">=</tt><tt id="link-31" class="py-name"><a title="ijtools.getImage" class="py-name" href="#" onclick="return doclink('link-31', 'getImage', 'link-0');">getImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line">    <tt class="py-name">im</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Function ijtools.updateAndDraw()=ijtools-module.html#updateAndDraw"><a title="ijtools.updateAndDraw" class="py-name" href="#" onclick="return doclink('link-32', 'updateAndDraw', 'link-32');">updateAndDraw</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line"> </tt>
<a name="error"></a><div id="error-def"><a name="L287"></a><tt class="py-lineno">287</tt> <a class="py-toggle" href="#" id="error-toggle" onclick="return toggle('error');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#error">error</a><tt class="py-op">(</tt><tt class="py-param">msg</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="error-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="error-expanded"><a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line"><tt class="py-docstring">    Displays a message in a dialog box with the specified title.</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line"><tt class="py-docstring">    @param msg: message to be displayed</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line"><tt class="py-docstring">    @type msg: str</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line"><tt class="py-docstring">    @param title: dialog box title</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line"><tt class="py-docstring">    @type title: str</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">title</tt><tt class="py-op">!=</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="ijtools.error" class="py-name" href="#" onclick="return doclink('link-33', 'error', 'link-1');">error</a></tt><tt class="py-op">(</tt><tt class="py-name">title</tt><tt class="py-op">,</tt> <tt class="py-name">msg</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="ijtools.error" class="py-name" href="#" onclick="return doclink('link-34', 'error', 'link-1');">error</a></tt><tt class="py-op">(</tt><tt class="py-name">msg</tt><tt class="py-op">)</tt> </tt>
</div><a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line"> </tt>
<a name="getDirectory"></a><div id="getDirectory-def"><a name="L301"></a><tt class="py-lineno">301</tt> <a class="py-toggle" href="#" id="getDirectory-toggle" onclick="return toggle('getDirectory');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#getDirectory">getDirectory</a><tt class="py-op">(</tt><tt class="py-param">title</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="getDirectory-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="getDirectory-expanded"><a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line"><tt class="py-docstring">    Returns the path to the home ("user.home"), startup (ImageJ directory),</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line"><tt class="py-docstring">    plugins, macros, temp, current or image directory if title is "home",</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line"><tt class="py-docstring">    "startup", "plugins", "macros", "temp", "current" or "image", </tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line"><tt class="py-docstring">    otherwise, displays a dialog and returns the path to the directory</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line"><tt class="py-docstring">    selected by the user.</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line"><tt class="py-docstring">    @type title: str</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: str</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Function ijtools.getDirectory()=ijtools-module.html#getDirectory"><a title="ijtools.getDirectory" class="py-name" href="#" onclick="return doclink('link-35', 'getDirectory', 'link-35');">getDirectory</a></tt><tt class="py-op">(</tt><tt class="py-name">title</tt><tt class="py-op">)</tt> </tt>
</div><a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line"> </tt>
<a name="openBrowser"></a><div id="openBrowser-def"><a name="L315"></a><tt class="py-lineno">315</tt> <a class="py-toggle" href="#" id="openBrowser-toggle" onclick="return toggle('openBrowser');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#openBrowser">openBrowser</a><tt class="py-op">(</tt><tt class="py-param">url</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="openBrowser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="openBrowser-expanded"><a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line"><tt class="py-docstring">    Attempts to open the default web browser to the given URL.</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line"><tt class="py-docstring">    @param url: url to open</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line"><tt class="py-docstring">    @type url: str</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">plugin</tt><tt class="py-op">.</tt><tt class="py-name">BrowserLauncher</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line">    <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">plugin</tt><tt class="py-op">.</tt><tt class="py-name">BrowserLauncher</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">openURL</tt><tt class="py-op">(</tt><tt class="py-name">url</tt><tt class="py-op">)</tt> </tt>
</div><a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line">     </tt>
<a name="setTitle"></a><div id="setTitle-def"><a name="L326"></a><tt class="py-lineno">326</tt> <a class="py-toggle" href="#" id="setTitle-toggle" onclick="return toggle('setTitle');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#setTitle">setTitle</a><tt class="py-op">(</tt><tt class="py-param">title</tt><tt class="py-op">,</tt> <tt class="py-param">im</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="setTitle-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="setTitle-expanded"><a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line"><tt class="py-docstring">    Sets the image name.</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line"><tt class="py-docstring">    @param title: image title to be set</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line"><tt class="py-docstring">    @type title: str</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line"><tt class="py-docstring">    @param im: ImageJ ImagePlus to use, if 'None' use the current select image.</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line"><tt class="py-docstring">    @type im: ImageJ ImagePlus</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: None</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">im</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> <tt class="py-name">im</tt><tt class="py-op">=</tt><tt id="link-36" class="py-name"><a title="ijtools.getImage" class="py-name" href="#" onclick="return doclink('link-36', 'getImage', 'link-0');">getImage</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line">    <tt class="py-name">im</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Function ijtools.setTitle()=ijtools-module.html#setTitle"><a title="ijtools.setTitle" class="py-name" href="#" onclick="return doclink('link-37', 'setTitle', 'link-37');">setTitle</a></tt><tt class="py-op">(</tt><tt class="py-name">title</tt><tt class="py-op">)</tt> </tt>
</div><a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line"> </tt>
<a name="isWindows"></a><div id="isWindows-def"><a name="L340"></a><tt class="py-lineno">340</tt> <a class="py-toggle" href="#" id="isWindows-toggle" onclick="return toggle('isWindows');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#isWindows">isWindows</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="isWindows-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="isWindows-expanded"><a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line"><tt class="py-docstring">    Returns true if this machine is running Windows.</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: bool</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Function ijtools.isWindows()=ijtools-module.html#isWindows"><a title="ijtools.isWindows" class="py-name" href="#" onclick="return doclink('link-38', 'isWindows', 'link-38');">isWindows</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">     </tt>
<a name="isVista"></a><div id="isVista-def"><a name="L348"></a><tt class="py-lineno">348</tt> <a class="py-toggle" href="#" id="isVista-toggle" onclick="return toggle('isVista');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="ijtools-module.html#isVista">isVista</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="isVista-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="isVista-expanded"><a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line"><tt class="py-docstring">    Returns true if ImageJ is running on Windows Vista.</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line"><tt class="py-docstring">    @rtype: bool</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">ij</tt><tt class="py-op">.</tt><tt class="py-name">IJ</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Function ijtools.isVista()=ijtools-module.html#isVista"><a title="ijtools.isVista" class="py-name" href="#" onclick="return doclink('link-39', 'isVista', 'link-39');">isVista</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line"> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line"><tt class="py-name">rename</tt><tt class="py-op">=</tt><tt id="link-40" class="py-name"><a title="ijtools.setTitle" class="py-name" href="#" onclick="return doclink('link-40', 'setTitle', 'link-37');">setTitle</a></tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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